note
biohisham
So you basically have some coordinates and want to check if anyone of the alleles matches the location given by the coordinates right ? But your coordinates don't tell about which chromosome these alleles are expected but what you can probably do is download the chromosomes in say FastA format and then use <c>Bio::SeqIO</c> using the <c>subseq</c>
function.
<p>here is the documentation to the module [http://search.cpan.org/~cjfields/BioPerl-1.6.923/Bio/SeqIO.pm|Bio::SeqIO]</p>
<p>The <c>subseq</c> function requires a beginning and an end to what it is going to extract so probably you want to reformat your coordinates as follows <p><c>$seq->subseq(coordinate-1, coordinate+1)</c></p> to extract three bases with the middle one being the actual nucleotide you want to compare your alleles against.
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Note that BioPerl can be a bit slow and therefore consider using something like [http://manpages.ubuntu.com/manpages/hardy/man1/sfetch.1.html|sfetch] or <c>esl-sfetch</c> which will again require providing beginning and end positions to what it is to extract</p>
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David R. Gergen said "We know that second terms have historically been marred by hubris and by scandal." and I am a four y.o. monk...
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